Input and runtime details for job 6756176 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
71	0.00365	0.1656	b4478	dgoD	-6.42	0.153775	171 -- 195	38 -- 57	D-galactonate dehydratase	_____________170_______________________196\n_____________\|_________________________\|\n5'-AAA...GCAGC_______A____GUAUC________GUGCA...UGA-3'\n______________AUUUGUU_AGGC_____GAGAGGCA\n______________\|:\|\|\|:\|_\|:\|\|_____:\|\|\|:\|\|\|\n______________UGAACGA_UUCG_____UUCUUCGU\n3'-UUU...UACUU_______A_________________GAAUU...CAA-5'\n_____________\|_________________________\|\n_____________58________________________37\n	189 -- 195	38 -- 44	-17.6382 kcal/mol	5.02573 kcal/mol	6.19395 kcal/mol	170 196@LB@ \| \|@LB@5'-AAA...GCAGC A GUAUC GUGCA...UGA-3'@LB@ AUUUGUU AGGC GAGAGGCA@LB@ \|:\|\|\|:\| \|:\|\| :\|\|\|:\|\|\|@LB@ UGAACGA UUCG UUCUUCGU@LB@3'-UUU...UACUU A GAAUU...CAA-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -17.6382 kcal/mol@LB@Unfolding Energy - mRNA 5.02573 kcal/mol@LB@Unfolding Energy - sRNA 6.19395 kcal/mol@LB@@LB@Position - mRNA 171 -- 195@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 38 -- 44@LB@
196	0.02353	0.3864	b1948	fliP	-9.61	0.021211	171 -- 185	45 -- 59	flagellar biosynthesis protein	_____________170_____________186\n_____________\|_______________\|\n5'-AUU...AUGAA_______________UAGCG...GCG-3'\n______________AAAUUUGCUUAAGCG\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|:\n______________UUUGAACGAAUUCGU\n3'-UUU...CCUAC_______________UCUUC...CAA-5'\n_____________\|_______________\|\n_____________60______________44\n	178 -- 184	46 -- 52	-18.3894 kcal/mol	2.75936 kcal/mol	6.02152 kcal/mol	170 186@LB@ \| \|@LB@5'-AUU...AUGAA UAGCG...GCG-3'@LB@ AAAUUUGCUUAAGCG@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|:@LB@ UUUGAACGAAUUCGU@LB@3'-UUU...CCUAC UCUUC...CAA-5'@LB@ \| \|@LB@ 60 44@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -18.3894 kcal/mol@LB@Unfolding Energy - mRNA 2.75936 kcal/mol@LB@Unfolding Energy - sRNA 6.02152 kcal/mol@LB@@LB@Position - mRNA 171 -- 185@LB@Position - sRNA 45 -- 59@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 46 -- 52@LB@
18	0.0004863	0.08107	b2217	rcsB	-10.91	0.008593	172 -- 193	39 -- 59	response regulator in two-component regulatory system with RcsC and YojN	_____________171____________________194\n_____________\|______________________\|\n5'-AAC...GUCAA_________GU_______U___CUAUU...GCG-3'\n______________GAGCUUGCU__AGCAAGG_AGC\n______________:\|:\|\|\|\|\|\|__\|\|\|\|\|\|:_\|\|\|\n______________UUUGAACGA__UCGUUCU_UCG\n3'-UUU...CCUAC_________AU___________UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	183 -- 189	42 -- 48	-25.4912 kcal/mol	8.43277 kcal/mol	6.15149 kcal/mol	171 194@LB@ \| \|@LB@5'-AAC...GUCAA GU U CUAUU...GCG-3'@LB@ GAGCUUGCU AGCAAGG AGC@LB@ :\|:\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ UUUGAACGA UCGUUCU UCG@LB@3'-UUU...CCUAC AU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -25.4912 kcal/mol@LB@Unfolding Energy - mRNA 8.43277 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 42 -- 48@LB@
188	0.02199	0.3768	b3774	ilvC	-7.43	0.085257	172 -- 181	37 -- 46	ketol-acid reductoisomerase NAD(P)-binding	_____________171________182\n_____________\|__________\|\n5'-AUG...AACAA__________AACAU...GCU-3'\n______________UAAGAAGCAC\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	175 -- 181	37 -- 43	-13.663 kcal/mol	1.01181 kcal/mol	5.21654 kcal/mol	171 182@LB@ \| \|@LB@5'-AUG...AACAA AACAU...GCU-3'@LB@ UAAGAAGCAC@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -13.663 kcal/mol@LB@Unfolding Energy - mRNA 1.01181 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 172 -- 181@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 37 -- 43@LB@
65	0.003382	0.1645	b1739	osmE	-4.35	0.428849	173 -- 228	7 -- 58	osmotically-inducible lipoprotein	_____________172______________________________________________________229\n_____________\|________________________________________________________\|\n5'-GAA...UAUCU___AC___GA___A_______A__GAAUAUGAACAAGAA____G______U_____GUGCA...AGC-3'\n______________AAC__GCU__UAA_CAAGAGG_CG_______________UAUG_CAGGAA_UCUGA\n______________\|\|\|__\|\|\|__\|\|\|_\|\|\|\|\|:\|_\|:_______________\|\|::_\|\|\|\|\|\|_\|\|\|\|\|\n______________UUG__CGA__AUU_GUUCUUC_GU_______________AUGU_GUCCUU_AGACU\n3'-UUU...CUACU___AA________C__________GAAUUUUUUAAGCA_____G______U_____ACACAA-5'\n_____________\|________________________________________________________\|\n_____________59_______________________________________________________6\n	187 -- 193	40 -- 46	-28.7812 kcal/mol	10.5809 kcal/mol	13.8467 kcal/mol	172 229@LB@ \| \|@LB@5'-GAA...UAUCU AC GA A A GAAUAUGAACAAGAA G U GUGCA...AGC-3'@LB@ AAC GCU UAA CAAGAGG CG UAUG CAGGAA UCUGA@LB@ \|\|\| \|\|\| \|\|\| \|\|\|\|\|:\| \|: \|\|:: \|\|\|\|\|\| \|\|\|\|\|@LB@ UUG CGA AUU GUUCUUC GU AUGU GUCCUU AGACU@LB@3'-UUU...CUACU AA C GAAUUUUUUAAGCA G U ACACAA-5'@LB@ \| \|@LB@ 59 6@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -28.7812 kcal/mol@LB@Unfolding Energy - mRNA 10.5809 kcal/mol@LB@Unfolding Energy - sRNA 13.8467 kcal/mol@LB@@LB@Position - mRNA 173 -- 228@LB@Position - sRNA 7 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
93	0.006966	0.2379	b0436	tig	-6.81	0.123164	173 -- 190	25 -- 42	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________172________________191\n_____________\|__________________\|\n5'-UAC...UGACC_______GU__UUU____AGGUA...UCA-3'\n______________GAGCACU__GA___UUUG\n______________:\|\|\|\|\|\|__:\|___\|\|:\|\n______________UUCGUGA__UU___AAGC\n3'-UUU...CGUUC_______AU__UUU____AAUGU...CAA-5'\n_____________\|__________________\|\n_____________43_________________24\n	173 -- 179	36 -- 42	-10.673 kcal/mol	2.21437 kcal/mol	1.64855 kcal/mol	172 191@LB@ \| \|@LB@5'-UAC...UGACC GU UUU AGGUA...UCA-3'@LB@ GAGCACU GA UUUG@LB@ :\|\|\|\|\|\| :\| \|\|:\|@LB@ UUCGUGA UU AAGC@LB@3'-UUU...CGUUC AU UUU AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -10.673 kcal/mol@LB@Unfolding Energy - mRNA 2.21437 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 173 -- 190@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 36 -- 42@LB@
47	0.002119	0.1452	b0694	kdpE	-6.96	0.113004	177 -- 189	26 -- 38	response regulator in two-component regulatory system with KdpD	_____________176___________190\n_____________\|_____________\|\n5'-ACG...CCUGA_____________CAUGA...CGC-3'\n______________ACUUGAAGAAUUU\n______________\|\|\|\|:\|\|:\|\|\|\|:\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	179 -- 185	30 -- 36	-10.6038 kcal/mol	2.21135 kcal/mol	1.43364 kcal/mol	176 190@LB@ \| \|@LB@5'-ACG...CCUGA CAUGA...CGC-3'@LB@ ACUUGAAGAAUUU@LB@ \|\|\|\|:\|\|:\|\|\|\|:@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -10.6038 kcal/mol@LB@Unfolding Energy - mRNA 2.21135 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 30 -- 36@LB@
39	0.00159	0.1292	b1637	tyrS	-8.51	0.043578	178 -- 203	5 -- 27	tyrosyl-tRNA synthetase	_____________177________________________204\n_____________\|__________________________\|\n5'-CAU...UGCAG_________A__U_______U_____GCAAG...CGA-3'\n______________UCGUUAUAU_CA_GGAGAUU_UGAUG\n______________\|\|\|\|\|\|:\|:_\|\|_\|\|\|:\|\|:_\|\|\|\|\|\n______________AGCAAUGUG_GU_CCUUUAG_ACUAC\n3'-UUU...UUUUA__________________________ACAA-5'\n_____________\|__________________________\|\n_____________28_________________________4\n	191 -- 197	10 -- 16	-22.7194 kcal/mol	5.60368 kcal/mol	8.60118 kcal/mol	177 204@LB@ \| \|@LB@5'-CAU...UGCAG A U U GCAAG...CGA-3'@LB@ UCGUUAUAU CA GGAGAUU UGAUG@LB@ \|\|\|\|\|\|:\|: \|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ AGCAAUGUG GU CCUUUAG ACUAC@LB@3'-UUU...UUUUA ACAA-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -22.7194 kcal/mol@LB@Unfolding Energy - mRNA 5.60368 kcal/mol@LB@Unfolding Energy - sRNA 8.60118 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
141	0.01363	0.3114	b0767	pgl	-6.62	0.137481	178 -- 199	36 -- 55	6-phosphogluconolactonase	_____________177____________________200\n_____________\|______________________\|\n5'-UCA...GUCAG_____A__U__A__________CAUGA...AUG-3'\n______________UUGCU_AA_GC_AAGGAGCAUU\n______________\|\|\|\|\|_\|\|_\|\|_\|\|\|:\|\|\|\|:\|\n______________AACGA_UU_CG_UUCUUCGUGA\n3'-UUU...CUUUG_____A________________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	193 -- 199	36 -- 42	-19.0667 kcal/mol	6.27112 kcal/mol	6.17795 kcal/mol	177 200@LB@ \| \|@LB@5'-UCA...GUCAG A U A CAUGA...AUG-3'@LB@ UUGCU AA GC AAGGAGCAUU@LB@ \|\|\|\|\| \|\| \|\| \|\|\|:\|\|\|\|:\|@LB@ AACGA UU CG UUCUUCGUGA@LB@3'-UUU...CUUUG A AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.62 kcal/mol@LB@Hybridization Energy -19.0667 kcal/mol@LB@Unfolding Energy - mRNA 6.27112 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 178 -- 199@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter	_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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